Hello,
When carrying out the SplitNCigarReads command I'm getting the following error message:
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: SplitNCigarReads
My command is:
java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R Genome.fasta -I WAr7.dedupped.bam -o WAr7.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
I'm using java version 1.7.0_72 and gatk version 2.7-2 (also tried 3.2-2)
Thank you for your help,
Mark